The document describes the steps to perform a molecular dynamics simulation of lysozyme in water using GROMACS. It details installing GROMACS in Google Colab, uploading input files, running energy minimization, equilibration, and production simulations. It also describes analyzing the trajectory by calculating the root mean square deviation (RMSD) and radius of gyration (Rg) to monitor stability of the protein structure over time.

1. Lab#9: GROMACS:
Lysozyme in Water
Asian University For Women
BINF 3016: Protein Modeling
(Lab - Fall 2022)
Syed Mohammad Lokman
Instructor
Asian University for Women

2. GROMACS
grompp
mdrun
energy
rms
gyrate
trjconv

3. gmx grompp -f xyz1.mdp -c xyz2.gro -r xyz2.gro -p xyz3.top -o xyz4.tpr-
-f = input file
.mdp = contains
settings for the
process
-c = coordinate file
.gro = contains
coordinate of
molecules
-r = restrain file
.gro = contains
coordinate of
molecules
-p = process file
.top = contains
topology of
molecules
-o = output file
.tpr = input file for
mdrun process in
gmx

4. gmx grompp -f xyz1.mdp -c xyz2.gro -r xyz2.gro -p xyz3.top -o xyz4.tpr-
-f = input file
.mdp = contains
settings for the
process
-c = coordinate file
.gro = contains
coordinate of
molecules
-r = restrain file
.gro = contains
coordinate of
molecules
-p = process file
.top = contains
topology of
molecules
-o = output file
.tpr = input file for
mdrun process in
gmx
gmx mdrun -v -deffnm xyz4
● em.log: ASCII-text log file of the EM process
● em.edr: Binary energy file
● em.trr: Binary full-precision trajectory
● em.gro: Energy-minimized structure
generate

6. Step 1: Installing GROMACS in Google Colab
1. Open a new google colab notebook, and rename the notebook as “lab#9_YourID”.
2. Connect to runtime
3. Enable GPU: From the top menu:
1. Runtime> Change Runtime Type> “GPU” under Hardware Accelerator option > Save (N.B.: If a prompt ask to
terminate other active runtime, do accordingly. Terminate the other runtime.)
4. Install GROMACS by using following code in the google colab:
# Download and unzip the compressed folder of GROMACS 2020.6 version
!wget https://raw.githubusercontent.com/pb3lab/ibm3202/master/software/gromacs.tar.gz
!tar xzf gromacs.tar.gz
# It is recommended to upgrade cmake
!pip install cmake --upgrade
!ln -sf /content/gromacs/bin/gmx /usr/bin/
!gmx --version
#Installing py3Dmol and biopython
!pip install py3Dmol biopython
#Importing py3Dmol for safety
import py3Dmol
#Make a new directory named "lab9"
%mkdir /content/lab9
#Change directory to "lab9"
%cd /content/lab9
#Check present working directory
!pwd

7. Step 2: Uploading Input files to Google Colab
1. Unzip the input files generated by Charmm-GUI.
2. Inside “charmm-gui” folder, find “gromacs” folder containing the necessary input files for MD production in GROMACS.
3. Upload these files inside lab9 folder. In your working google colab notebook, a folder named “lab9” is already created in the
previous step using “mkdir” command. (N.B.: to upload “toppar” folder, you have to create a folder named “toppar” first,
then upload the “toppar” folder files accordingly.)

8. ● Energy Minimization
● Equilibration
● MD Production
● Convert Trajectory
%%bash
gmx grompp -f step4 .0_minimization.mdp -c step3_input.gro -r step3_input.gro -p topol.top -n index.ndx -o em.tpr
gmx mdrun -v -deffnm em -nb gpu
%%bash
gmx grompp -f step4.1_equilibration.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
gmx mdrun -v -deffnm nvt -nb gpu
%%bash
gmx grompp -f step5_production.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o md.tpr
gmx mdrun -v -deffnm md -nb gpu
#Using trjconv to extract only the protein atoms from the simulation trajectory
!echo "Protein" > options
!echo "Protein" >> options
!echo " "
!gmx trjconv -s md.tpr -f md.xtc -o md_protPBC.pdb -pbc mol -center < options
!gmx trjconv -s md.tpr -f md.xtc -o md_protPBC.xtc -pbc mol -center < options

9. ● Analysis: RMSD
● Analysis: Gyration
!gmx rms -s md.tpr -f md_protPBC.xtc -o rmsd.xvg -tu ns
#The radius of gyration of a protein is a measure of its compactness.
#If a protein is stably folded, it will likely maintain a relatively steady value of Rg.
#If a protein unfolds, its Rg will change over time. Let's analyze the radius of
gyration for lysozyme in our simulation:
!gmx gyrate -s md.tpr -f md_protPBC.xtc -o gyrate.xvg

10. ● Analysis: RMSD
● Analysis: Gyration
!gmx rms -s md.tpr -f md_protPBC.xtc -o rmsd.xvg -tu ns
#The radius of gyration of a protein is a measure of its compactness.
#If a protein is stably folded, it will likely maintain a relatively steady value of Rg.
#If a protein unfolds, its Rg will change over time. Let's analyze the radius of
gyration for lysozyme in our simulation:
!gmx gyrate -s md.tpr -f md_protPBC.xtc -o gyrate.xvg

11. Thank You